BN1960 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.8058e-06 3.0333e-02
Layer 4 6.4320e-06 2.5960e-04
Layer 5 2.4140e-05 2.0326e-04
Layer 6 2.2759e-04 3.2058e-03
Layer 2 7.4685e-02 2.3577e-01
Layer 1 7.5976e-01 5.9810e-01
WM 9.0163e-01 5.2065e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SLC24A2 Expression Distribution
Gene Specificity Score (GSS)
SLC24A2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SLC24A2 Layer 4 2.7275 0.8329
ITPK1 Layer 4 2.7598 0.8313
SPOCK1 Layer 4 2.7793 0.8221
PINK1 Layer 5 2.5449 0.8193
TTC9B Layer 4 2.9160 0.8181
PRDX5 Layer 5 2.7422 0.8136
BMERB1 Layer 5 2.8623 0.8124
FKBP8 Layer 5 2.6279 0.8083
FBXW7 Layer 5 2.4941 0.8082
CAPNS1 Layer 5 2.5244 0.8077
SLC9A6 Layer 5 2.4727 0.8076
CTSD Layer 5 2.5723 0.8069
TOLLIP Layer 4 2.8174 0.8068
SIRPA Layer 4 2.5605 0.8063
RBX1 Layer 4 2.5420 0.8060
CYCS Layer 4 2.6367 0.8056
SYT4 Layer 5 2.8652 0.8052
UBE2M Layer 4 2.5898 0.8045
SSBP3 Layer 5 2.6777 0.8041
CEND1 Layer 5 2.6367 0.8019
MRPS21 Layer 4 2.6016 0.8006
NDRG4 Layer 5 2.7539 0.7990
SNAP91 Layer 5 2.6250 0.7978
TPPP Layer 5 2.3750 0.7972
GNB1 Layer 5 2.3555 0.7971
PRKAR1B Layer 5 2.7939 0.7954
PODXL2 Layer 4 2.4648 0.7943
DCLK1 Layer 5 2.7070 0.7940
NDUFV2 Layer 4 2.2900 0.7938
SEZ6L2 Layer 4 2.7393 0.7928
PFKP Layer 5 2.7822 0.7924
SYP Layer 5 2.7852 0.7916
IQSEC1 Layer 5 2.5391 0.7915
TUBB3 Layer 5 2.5479 0.7915
CHGA Layer 4 3.1602 0.7912
C9orf16 Layer 5 2.4941 0.7909
SYN1 Layer 5 2.5508 0.7906
PJA2 Layer 5 2.5176 0.7902
SH3GL2 Layer 5 2.6250 0.7899
PDXP Layer 5 2.6631 0.7898
NUDT4 Layer 5 2.7656 0.7893
MICOS10 Layer 5 2.5723 0.7891
LY6E Layer 5 2.5088 0.7887
RGS4 Layer 5 2.7715 0.7887
TPI1 Layer 5 2.4883 0.7883
STMN2 Layer 5 2.7598 0.7880
CANX Layer 5 2.4453 0.7877
MYO5A Layer 5 2.8398 0.7875
YPEL3 Layer 5 2.6162 0.7874
NDUFB8 Layer 5 2.5693 0.7874

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1960
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1960_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1960/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1960/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1960/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1960/report/PD/BN1960_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1960/report/PD/BN1960_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:17:27
  • Number of Processes: 10
  • Spending Time: 0h 3m